A Bradford school has robustly defended itself against “serious failings” that were laid bare by a Department for Education (DfE) report.

Kings Science Academy pointed to the “unprecedented pace” of opening and a “lack of training and support available for new governors” in a statement on its website.

The flagship free school, in Lidget Green, was the subject of a top-level probe which uncovered financial failings – including the disappearance of tens of thousands of pounds – false invoicing, and questionable staff appointments and payments.

But a statement on the school website read: “Two years ago the academy started with a strong mission to tackle educational inequality and to offer a first-class education to children living in deprived areas of inner-city Bradford.

“The financial and governance systems were initially very weak due to the unprecedented pace of opening the school within two or three months from approval and the lack of training and support available for new governors.

“It is of no surprise that the draft EFA report has highlighted some weaknesses with regards to the financial systems and governance two years ago in their historical review.

“Alongside this review, the principal also instigated a full and thorough internal review of finance and governance using Crow Clark and Whitehill. This review also identified areas for developments and further improvements.”

It added: “There has been no misappropriation of funds and all expenditure has been academy related.”

The school claims improvements in finance and governance systems have been achieved, and points to a “positive July 2013 report from the EFA on finance and governance”, a Deloitte audit report (2011-2012) which “highlighted how strengths and improvement were evolving”, and the external governance audit report (September 2013) from Bradford Council.

The statement continued: “The academy is now currently being monitored and challenged by a very effective governing body and there are strong financial control systems in place.”

DfE auditors were called in to examine the books after concerns were raised by a whistleblower about the way it was being run since it opened in September 2011.

The investigators found failings in the financial controls which has led to almost £77,000 of £183,000 Government start-up cash still being unaccounted for and now having to be paid back.

The probe also found the principal Sajid Hussain Raza had employed members of his family at the school.